The problem is not space...
I am having a hell with TextWrangler as I find out that this application
simply doesn't convert to Unix LF, so when I copied a file in terminal and
open it with twedit is Mac CR EOL and it causes problems with compilations
and makes.
Does anyone know a good reliable, simple editor in Mac that simply assure me
that I am working with Unix LF files no matter was the input EOL format?
Thanks,
Alan
On Thu, Apr 29, 2010 at 16:50, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> On Thu, Apr 29, 2010 at 11:18 AM, Alan <alanwilter.gmail.com> wrote:
>
> > Hi there,
> >
> > So compilation of Amber11 with mpi was going fine and the I got this:
> >
> > mpif90 -opmemd gbl_constants.o gbl_datatypes.o state_info.o
> file_io_dat.o
> > mdin_ctrl_dat.o mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o
> > inpcrd_dat.o
> > dynamics_dat.o img.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o
> > pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o
> > pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o
> > nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o
> dihedrals.o
> > extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o
> > constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o
> > pmemd_lib.o runfiles.o file_io.o bintraj.o pmemd_clib.o pmemd.o random.o
> > degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o
> > pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o
> > nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o charmm.o
> > charmm_gold.o ../../netcdf/lib/libnetcdf.a
> > ld: unknown option: -opmemd
> > collect2: ld returned 1 exit status
> > make: *** [pmemd] Error 1
> >
> > Clearly is should be:
> > mpif90 -o pmemd gbl_constants.o ...
> >
>
> It's a little strange that you got this error (I haven't gotten it on any
> systems I tried building on), however, here is, in my opinion, the most
> logical explanation.
>
> This has to do with LDOUT defined at the bottom of your config.h file.
> Mine
> says: LDOUT= -o . For me, there is a space after the -o in my config.h
> file. If we then look at $AMBERHOME/src/pmemd/src/Makefile, we see the
> lines:
>
> pmemd$(SFX): $(NETCDF) $(OBJS)
> $(PMEMD_LD) $(PMEMD_OPTFLAGS) $(LDOUT)$. $(OBJS) $(PMEMD_NETCDFLIB)
> $(LDFLAGS) $(PMEMD_FLIBSF)
>
> Notice that there is no space between $(LDOUT) and $.. This is undoubtedly
> the error you ran into. I think it would be a better idea to simply put a
> space between those options in the Makefile, but perhaps there is a good
> reason why that's not done (i.e. for compatibility with other, non-GNU
> unices? I have no experience with those). My guess is that something
> removed that extra space at the end of -o in your config.h file...
>
> Ross and/or other developers, should we patch the Makefile to put a space
> there? (and the same for pmemd.MPI and pmemd.cuda as well)
>
> All the best,
> Jason
>
>
> > and when do this by hand all goes fine. But, trying to pinpoint the error
> > was very challenging for me so I could solve that.
> >
> > Cheers,
> >
> > Alan
> > --
> > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> > Department of Biochemistry, University of Cambridge.
> > 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> > >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Thu Apr 29 2010 - 09:30:03 PDT
